Fig. 3: EEC lineage formation and composition in homeostasis and upon HFHSD.
From: Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice
a, Colour-coded UMAP plot of 2,865 EEC lineage cells from CD- and HFHSD-derived samples. Cluster annotation was based on known marker genes and labelling of mature EEC subtypes as previously described17. b, Expression levels of selected EEC markers (hormones and transcription factors) across EEC clusters plotted in UMAP space. c, Streamline plot of RNA velocity projected into UMAP space showing the direction of cell differentiation along trajectories for the endocrine lineage in CD-derived samples. Arrows indicate estimated future states of cells. d, Heatmap showing mean expression values per cluster of genes upregulated in EEP clusters during endocrine lineage formation. Genes were selected from (pan)endocrine, lineage- and stage-specific markers (Methods). Colour bars on the side indicate expression in the progenitor populations (Fig. 3a). e, Cell proportions in EEC lineage subsets from CD- and HFHSD-derived samples (mean ± s.e.m. of biologically independent samples, n = 3 mice per group, Dirichlet multinomial model). *Indicates a credible shift (95% highest posterior density interval of the frequency shift modeled by a Dirichlet multinomial model does not overlap 0). f–o, Validation of EEC frequencies in CD- and HFHSD-fed FVF mice by immunofluorescence staining. Representative LSM images (f) and quantification of Ngn3+ cells in isolated small intestinal crypts (g). Scale bar, 10 µm, n = 4 mice per group. Representative LSM images (h) and quantification of 5-HT+ cells in isolated small intestinal crypts (i). Scale bar, 10 µm, n = 4 mice per group. Representative LSM images (j) and quantification of Ghrl+ cells in duodenal sections (k–m). Scale bar, 100 µm; crypt, n = 5 for CD mice and n = 4 HFHSD mice; villus, n = 4 CD and HFHSD mice. Quantification of Gcg+ cells in ileal sections (n,o), n = 3 CD and HFHSD mice. Data are shown as mean ± s.e.m. of biologically independent samples. Statistical significance was determined by two-tailed Student’s t-test.
